On Friday (9/27/13) I ran the trails of Wilderness Lodge & Fort Wilderness Lodge. I was able to log 4 miles with the course. Here is the official flier Disney puts out on the running trail, but you have a lot of options to branch off on to, to add extra mileage.
Here is my Garmin data on my run, and a map of my run.
Here are some pictures I took during the run.
Throughout the run I saw lots of wildlife.
Near the end I took a gravel trail along Bay Lake back to the Wilderness Lodge.
Here are some details of the run from www.allears.net:
Fort Wilderness Campground
Wilderness Swamp Trail offers runners/walkers a wonderful opportunity to enjoy the primitive nature of this part of Florida. Begin at the Fort Wilderness Trading Post and follow the gravel road through the woods along the edge of Bay Lake for about 400 yards. The path crosses a small bridge, which is where the Swamp Trail actually begins. This trail winds throughout an actual swamp. All along both the path and the trail you are surrounded by cypress trees draped with Spanish Moss. The swamp trail is comprised of sandy soil which is refreshing to your legs, but can require extra care for proper footing. This part of the trail is roughly 500 yards, for a total out and back distance of approximately 1.1 miles.
Fort Wilderness also boasts a Fitness Trail/Bike Path, which begins just past the petting farm. Crossing the road, the paved path begins. It meanders along, running parallel to West Wilderness Road, eventually arriving at Wilderness Lodge. Along the way, the path is shaded by tall pine trees, covered with Spanish Moss. Because the path is shared by pedestrians and cyclists alike, caution must be used for safety. The width of the path, and the lines of sight for users of this delightful course add greatly to making it as safe as it is refreshing.
The Wilderness Lodge Nature Trail begins behind the lodge at the boat rental area. As with the Swamp Trail at FW Lodge, this path is sandy soil which is very easy on your legs. The trail runs behind the Wilderness Lodge Villas, then turns right and intersects with the Fitness Trail/Jogging Path. A sign indicates that going left will take you to the FW Campground, and going to the right will take you to the bus stop in front of Wilderness Lodge.
During spring and summer months, the trails and paths at both FW Campground and Wilderness Lodge will have gnats and mosquitoes. This is to be expected, as they run along Bay Lake and pass through a wetlands area. This situation will be worst during the early morning and early evening hours. Despite this fact, these paths and trails are among the most pleasant for walking or running at any of the Disney World resorts. Because these parts are relatively well shaded, they can be suitable for use even during the hotter parts of the day, while other family members are either napping or enjoying the swimming pools.